Try adding --invertmtx to the mri_label2vol command. I don't think the label2label command does anything, does it? Also, you might have better alignment if you run recon-all on the mni152 brain, then use mri_label2label to map the label from the individual into the 152 space using the surface transform, then convert that to the volume.
On 11/30/2015 10:13 AM, Francesca Strappini wrote: > Dear FreeSurfer experts, > > I'm trying to convert some retinotopic labels I created on the surface > of each individual subject to MNI305 space for FSL. > > I run the following commands, but the output is not registered > correctly. It seems to be shifted downward. > > mni152reg --s LG > > mri_label2label --srclabel lh.V1dorsalLG.label --s LG --regmethod > surface --trglabel lh.V1dorsalLG_new.label --hemi lh > > mri_label2vol --label lh.V1dorsalLG_new.label --reg > /usr/local/freesurfer/subjects/LG/mri/mni152.orig.mgz.reg --temp > /usr/share/fsl/data/standard/MNI152_T1_2mm.nii.gz --o > lh.V1dorsalLG_new_MNI.nii.gz > > Thanks for your help, > Francesca > > -- > Francesca Strappini, Ph.D. > Neurobiology Department > Weizmann Institute of Science > 234 Herzl Street, Rehovot 7610001 Israel > Tel.: +972 58 444 2584 > E-mail: francesca.strapp...@weizmann.ac.il > <mailto:francesca.strapp...@weizmann.ac.il> > > > _______________________________________________ > Freesurfer mailing list > Freesurfer@nmr.mgh.harvard.edu > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer -- Douglas N. Greve, Ph.D. MGH-NMR Center gr...@nmr.mgh.harvard.edu Phone Number: 617-724-2358 Fax: 617-726-7422 Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2 www.nmr.mgh.harvard.edu/facility/filedrop/index.html Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/ _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
